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- PDB-5t2t: Crystal structure of Lymphocytic choriomeningitis mammarenavirus ... -

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Basic information

Entry
Database: PDB / ID: 5t2t
TitleCrystal structure of Lymphocytic choriomeningitis mammarenavirus endonuclease bound to compound L742001
ComponentsRNA-directed RNA polymerase L
KeywordsTRANSFERASE / mammarenavirus / LCMV / endonuclease / inhibitor
Function / homology
Function and homology information


RNA-templated viral transcription / negative stranded viral RNA replication / cap snatching / virion component / host cell cytoplasm / Hydrolases; Acting on ester bonds / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / metal ion binding
Similarity search - Function
Arenavirus RNA polymerase / RNA polymerase, arenaviral / RNA endonuclease, cap-snatching / Arenavirus RNA polymerase / Arenavirus cap snatching domain / : / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-0N8 / : / RNA-directed RNA polymerase L / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesLymphocytic choriomeningitis mammarenavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.967 Å
AuthorsSaez-Ayala, M. / Yekwa, E.L. / Canard, B. / Alvarez, K. / Ferron, F.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-11-BSV8-0019 France
CitationJournal: IUCrJ / Year: 2018
Title: Crystal structures ofLymphocytic choriomeningitis virusendonuclease domain complexed with diketo-acid ligands.
Authors: Saez-Ayala, M. / Yekwa, E.L. / Carcelli, M. / Canard, B. / Alvarez, K. / Ferron, F.
History
DepositionAug 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 9, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3May 30, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-directed RNA polymerase L
B: RNA-directed RNA polymerase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,26911
Polymers47,4442
Non-polymers8259
Water6,233346
1
A: RNA-directed RNA polymerase L
hetero molecules

B: RNA-directed RNA polymerase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,26911
Polymers47,4442
Non-polymers8259
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_345-x-2,-y-1,z+1/21
Buried area4070 Å2
ΔGint-67 kcal/mol
Surface area20350 Å2
MethodPISA
2
B: RNA-directed RNA polymerase L
hetero molecules

A: RNA-directed RNA polymerase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,26911
Polymers47,4442
Non-polymers8259
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_344-x-2,-y-1,z-1/21
Buried area4070 Å2
ΔGint-67 kcal/mol
Surface area20350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.116, 108.116, 54.087
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein RNA-directed RNA polymerase L / Protein L


Mass: 23722.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymphocytic choriomeningitis mammarenavirus
Gene: L, KUE_IGS310002 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A059U382, UniProt: P14240*PLUS, RNA-directed RNA polymerase

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Non-polymers , 6 types, 355 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-0N8 / (2Z)-4-[1-benzyl-4-(4-chlorobenzyl)piperidin-4-yl]-2-hydroxy-4-oxobut-2-enoic acid


Mass: 413.894 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H24ClNO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.444 Å3/Da / Density % sol: 64.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Na citrate 0,1M, Isopropanol 3,5%, MnCl2 1mM, L742001 2mM

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.967→54.06 Å / Num. obs: 44686 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.998 / Net I/σ(I): 12.51
Reflection shellResolution: 1.967→2.037 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.02 / CC1/2: 0.715 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimless0.5.15data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JSB

3jsb


Resolution: 1.967→54.058 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2214 2210 4.95 %
Rwork0.1825 --
obs0.1845 44691 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.967→54.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3144 0 47 346 3537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083308
X-RAY DIFFRACTIONf_angle_d1.1554448
X-RAY DIFFRACTIONf_dihedral_angle_d14.3291270
X-RAY DIFFRACTIONf_chiral_restr0.041495
X-RAY DIFFRACTIONf_plane_restr0.004578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9667-2.00950.31161640.26642630X-RAY DIFFRACTION100
2.0095-2.05620.28191480.26262587X-RAY DIFFRACTION100
2.0562-2.10770.27721400.23652639X-RAY DIFFRACTION100
2.1077-2.16470.31131230.23082689X-RAY DIFFRACTION100
2.1647-2.22840.26161500.21522580X-RAY DIFFRACTION100
2.2284-2.30030.24561330.21742648X-RAY DIFFRACTION100
2.3003-2.38250.28571300.21272649X-RAY DIFFRACTION100
2.3825-2.47790.23911210.20032668X-RAY DIFFRACTION100
2.4779-2.59070.25071300.19692659X-RAY DIFFRACTION100
2.5907-2.72720.23221470.1942643X-RAY DIFFRACTION100
2.7272-2.89810.2521140.19292662X-RAY DIFFRACTION100
2.8981-3.12180.22791080.18392694X-RAY DIFFRACTION100
3.1218-3.4360.19591330.16822640X-RAY DIFFRACTION100
3.436-3.9330.20471620.16352680X-RAY DIFFRACTION100
3.933-4.95470.17211470.14432684X-RAY DIFFRACTION100
4.9547-54.07840.2051600.17332729X-RAY DIFFRACTION100

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